#!/usr/bin/perl
use strict;
use warnings;

use Data::Dumper;
use Modules::Utilities;
use Modules::GTF2fasta;
use Modules::LongORF;
use Modules::AddCDSs;

my $conf_file = "conf/conf1.txt";

print "Welcome to TGAC's longorf_pipeline!\n";

my $util  = Modules::Utilities->new;
   $util->read_conf_file($conf_file);
my $gtf   = Modules::GTF2fasta->new($util);
   $gtf->run;
my $fas   = Modules::LongORF->new($util);
my $orfs  = $fas->run;    
my $cdss  = Modules::AddCDSs->new($util);
   $cdss->run($orfs);
#print Dumper $orfs;

print "\nlongorf_pipeline finished\n";
print "TIME ELAPSED: " . $util->time_elapsed . " seconds.\n";